Setting parameters

All parameter settings for enrichment are kept in a single Matlab structure. It can be set to default values as:

enrichmentParams = GiveMeDefaultEnrichmentParams();

You can alter the properties of the enrichment analysis by altering the parameter values set in GiveMeDefaultEnrichmentParams (this will ensure accurate filenames, determined within GiveMeDefaultEnrichmentParams).

Some example parameters:

• dataSource, specifies the source of GO annotations, to be loaded using GetFilteredGOData. Options are mouse-direct (hierarchy and annotations taken directly from GO), human-direct (hierarchy and annotations taken directly from GO), mouse-GEMMA (processed hierarchy and annotations downloaded from GEMMA).
• processFilter, a subset of GO processes to consider. Default: biological_process.
• sizeFilter, filter to a subset of GO categories by their number of annotations ('size'). Default is [5,200] (only consider GO categories with between 5 and 200 gene annotations).
• numSamples, number of iterations (1e4 is the default, can ramp up to get better significance estimates for small p-values).